X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.2
Temperature 291.0
Details Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM sodium citrate (pH 5.2), 1.25 M lithium sulfate, and 0.5 M ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.09 α = 90
b = 106.09 β = 90
c = 86.09 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD mirrors 2008-05-21
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97931 SSRL BL9-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3.1 30 97.7 0.104 0.081 -- 4.3 39168 38268 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.1 3.21 99.3 0.38 0.284 2.44 4.1 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 3.1 19.94 -- 2.0 39079 32319 3120 82.7 -- 0.193 0.193 0.245 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.1 3.21 -- 200 1773 0.331 0.36 0.025 50.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model OVERALL
Mean Isotropic B 68.1
Anisotropic B[1][1] 13.87
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 13.87
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -27.74
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.009
c_improper_angle_d 0.75
c_angle_deg 1.1
c_dihedral_angle_d 23.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.34
Luzzati Sigma A (Observed) 0.59
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.67
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5036
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 36

Software

Software
Software Name Purpose
CNS refinement version: 1.2
ADSC data collection version: Quantum
HKL-2000 data reduction
SCALEPACK data scaling
SHELX phasing version: then SOLVE/RESOLVE